I am new to pathway analysis , please kindly I would like to know what is significant pathway gene set, and what is mean by set size, for example if I have OXPHOS WHAT IS MEAN GENE SET OF IT?
I assume you know what oxidative phosphorylation is (if not, take a biochem class). There are a number of genes involved in this. A group of these genes (or anything else, for that matter) is called a set. The size of this set is the number of genes contained in it. Regarding significance, a set is significantly changed if your differentially expressed genes are enriched in members of the set (e.g., if you happened to have 10 differentially expressed genes and they were all in the OXPHOS set and that only had 10 members that this pathway would be significant...obviously you wouldn't need all members of a set to be DE for significance).
Dear Shawin,
well your post is a bit confusing. Probably if I can assume correctly and OXPHOS is a result from a pathway analysis you have already performed, OXPHOS could probably related to the metabolic pathway Oxidative phosphorylation. Anyway, pathway(or gene-set) analysis is a very general field, and you should first check some excellent and very informative articles:
Then, you could select a specific pathway methodology analysis that fit in your current project(like over-representation, GSEA, roast, pathway analysis with topology information etc.). Also, just to mention, some nice tools and databases with very curated gene-sets not restricted to pathway analysis, is the Broad Institute, the web-tool Enrichr, as also other numerous tools.
Finally, the term set size you mentioned above, probably refers to the total number of your input genes, or the number of the size of the background genes(the ones that are annotated to a query pathway you test for functional overrepresentation).
Hope this is helpful-Best,
Efstathios
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